Google Webmaster Tools Arghhhhh

I have a site which is a few weeks old. It is showing on Google for some really crappy keyphrases, but not for the ones I want.

So, I've had a look at Webmaster tools, and two things really worry me.

1. If I do an explorer of my site with yahoo it shows up 1,056 backlinks to my homepage, and 672 links to a subpage. However, in webmaster tool it shows up 700 backlinks to subpage, and only TWO backlinks to my homepage! I can see a massive list of sites linking to me....and none of them are linking to my homepage, just the subpage.

2. The list of keywords which Webmaster Tools is howing for my domain is way of what I want it to be. Im targetting a 4 word keyphrase, but webmaster tools is only showing ONE of the keywords. I havent stuffed keywords, but they are mentioned around 1.5-2%....but not a single mention is made of them in the webmaster tools keyword list.

Issue one is the one which really worries me....does it mean Google isnt seeing any backlinks to my homepage? Backlink watch is showing 2,200 backlinks, yahoo over 1,000, but my webmaster tools isnt including any of them....only the ones to a sub-page.

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